Goals:
install and become competent in using ProMol
put on the 6 laptops in lab (Windows) and install on the Linux distribution on one of the laptops too
Read some papers, websites, etc. on how to implement ProMol.
03/09/13
Tried installing ProMol on correct PyMol 1.3, but still nothing happens when I click on the ProMol plugin.
03/07/13
Error when installing ProMol on clean installation of PyMol 1.3r2 on Histidine laptop (resolved: use PyMol 1.3)
This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. Exception in plugin 'ProMol' -- Traceback follows... Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py", line 156, in initialize_plugins builtin.import(mod_name) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\ProMol\init.py", line 5, in ? from pmg_tk.startup.ProMol.promolglobals import VERSION File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\ProMol\promolglobals.py", line 777 self.widget.columnconfigure(0, weight=leftWeight if someOfEach else 1) ^ SyntaxError: invalid syntax Error: unable to initialize plugin 'ProMol'.
02/16/13 -
Another error when opening ProMol:
Error: 2
<type 'exceptions.ImportError'> Exception in Tk callback
Function: <function <lambda> at 0x7f7b84705de8> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in call
return apply(self.func, args)
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/init.py", line 18, in <lambda>
command = lambda p=pymol:GUI.init(p))
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/init.py", line 43, in init
from pmg_tk.startup.ProMol.GUI import welcome, ez_viz, motifs, \
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/motifs.py", line 5, in <module>
from pmg_tk.startup.treewidgets import widget, node, texttree
<type 'exceptions.ImportError'>: No module named treewidgets
Cannot find any 'treewidgets' file
Ruifei installed updated ProMol on personal laptop, running into error when installing ProMol:
Exception in plugin 'ProMol' -- Traceback follows...
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pmg_tk/PMGApp.py", line 315, in initializePlugins builtin.import(mod_name)
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/init.py", line 11, in <module>
from pmg_tk.startup.ProMol import GUI
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/init.py", line 7, in <module>
from pmg_tk.startup.remote_pdb_load import FetchPDB as showFetchDialog
ImportError: No module named remote_pdb_load
Error: unable to initialize plugin 'ProMol'.
FIX: copy contents of 'startup' directory from another directory if the current 'startup' directory does not contain the 'remote_pdb_load' file.
020713 - Ruifei and Dr. B met with Dr. Paul Craig about ProMol
Latest Version of ProMol is uploaded to Google Docs/Misc/Software/ProMOL_notPyMol
ProMOL-194.zip
Unzip this to the appropriate folder
ToDo:
Add specific instructions on how to install ProMol on a Windows computer
NOTE: the older ProMOL (not the 194 version) worked better with older version of PyMol (not the Schrodinger version - but rather the DeLano Scientific version)
Purpose: send PDB ID's and/or E.C. numbers of our enzymes to Dr. Paul Craig at RIT (Rochester Institute of Technology). He will have his students work on them.
Ruifei
Goals:
install and become competent in using ProMol
put on the 6 laptops in lab (Windows) and install on the Linux distribution on one of the laptops too
Read some papers, websites, etc. on how to implement ProMol.
03/09/13
Tried installing ProMol on correct PyMol 1.3, but still nothing happens when I click on the ProMol plugin.
03/07/13
Error when installing ProMol on clean installation of PyMol 1.3r2 on Histidine laptop (resolved: use PyMol 1.3)
This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
Exception in plugin 'ProMol' -- Traceback follows...
Traceback (most recent call last):
File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py", line 156, in initialize_plugins
builtin.import(mod_name)
File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\ProMol\init.py", line 5, in ?
from pmg_tk.startup.ProMol.promolglobals import VERSION
File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\ProMol\promolglobals.py", line 777
self.widget.columnconfigure(0, weight=leftWeight if someOfEach else 1)
^
SyntaxError: invalid syntax
Error: unable to initialize plugin 'ProMol'.
02/16/13 -
Another error when opening ProMol:
Error: 2
<type 'exceptions.ImportError'> Exception in Tk callback
Function: <function <lambda> at 0x7f7b84705de8> (type: <type 'function'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in call
return apply(self.func, args)
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/init.py", line 18, in <lambda>
command = lambda p=pymol:GUI.init(p))
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/init.py", line 43, in init
from pmg_tk.startup.ProMol.GUI import welcome, ez_viz, motifs, \
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/motifs.py", line 5, in <module>
from pmg_tk.startup.treewidgets import widget, node, texttree
<type 'exceptions.ImportError'>: No module named treewidgets
Cannot find any 'treewidgets' file
Ruifei installed updated ProMol on personal laptop, running into error when installing ProMol:
Exception in plugin 'ProMol' -- Traceback follows...
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/pmg_tk/PMGApp.py", line 315, in initializePlugins
builtin.import(mod_name)
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/init.py", line 11, in <module>
from pmg_tk.startup.ProMol import GUI
File "/usr/lib/python2.7/dist-packages/pmg_tk/startup/ProMol/GUI/init.py", line 7, in <module>
from pmg_tk.startup.remote_pdb_load import FetchPDB as showFetchDialog
ImportError: No module named remote_pdb_load
Error: unable to initialize plugin 'ProMol'.
FIX: copy contents of 'startup' directory from another directory if the current 'startup' directory does not contain the 'remote_pdb_load' file.
020713 - Ruifei and Dr. B met with Dr. Paul Craig about ProMol
Latest Version of ProMol is uploaded to Google Docs/Misc/Software/ProMOL_notPyMol
ProMOL-194.zip
Unzip this to the appropriate folder
2 ProMol Websites
http://www.rit.edu/cos/ezviz/ProMOL_dl.htmlThis one has updated version of ProMol
http://www.promol.org/
Link to ProMol User Guide
ProMOL_User_Guide.pdfToDo:
Add specific instructions on how to install ProMol on a Windows computer
NOTE: the older ProMOL (not the 194 version) worked better with older version of PyMol (not the Schrodinger version - but rather the DeLano Scientific version)
Catalytic Binding Site Atlas:
http://www.ebi.ac.uk/thornton-srv/databases/CSA/PART 1:
Purpose: send PDB ID's and/or E.C. numbers of our enzymes to Dr. Paul Craig at RIT (Rochester Institute of Technology). He will have his students work on them.INSTRUCTIONS:
InstructionsProMolProject_HomologyModels_v6.txt
- Mark each target as either:
- Homology Model needed
ORIf structure available, list PDB
If Homology Model needed, use SWISS-Model to find template, then use ICM to generate Homology Model.
Identities = , Positives =
PDB Identifier
2012 Targets
LeishmaniaTarget-serine-threonine protein phosphatase (Leishmania major)
Homology Model needed ---Joey--- DONE
Template: 2nppf
Sequence Identities = 207/284 (72%) , Positives = 239/284 (84%)
Template: Clash score, Molprobity score = 51.32, 3.47
Model: Clash score, Molprobity score = 18.24, 3.11
Wolbachia endosymbiont of Brugia malayi (see Wolbachia Targets page too)
Target - 1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR] (Wolbachia)
Homology Model needed - Dr. B - DONE
Template: 1R0k
Sequence Identities = 42.34% , Positives = 63%
Template: Clash score, Molprobity score = 13.66 , 1.77
Model: Clash score, Molprobity score = 3.85 , 2.11
Target - FabI enoyl-acyl-carrier-protein reductase NADH (Wolbachia)
Homology Model needed - JC - DONE
Template: 3K31-A
Sequence Identities = 66% 169/256 , Positives = 214/256 83%
Template: Clash score, Molprobity score = 4.08, 1.40
Model: Clash score, Molprobity score = 0.00 , 1.36
Yersinia
Target - Fab V (Yersinia Pestis)
PDB: 3ZU5 - Sadhana - DONE
Model: Clash score, Molprobity score = 11.63, 1.92
Target- Protein Tyrosine Phosphate (Yersinia Enterocolitica)
Homology Model needed - Sadhana - DONE
Template:1YWF-A
Sequence Identities = 28% , Positives = 42%
Template: Clash score, Molprobity score = 5.1, 2.03
Model: Clash score, Molprobity score = 13.04, 3.03
Francisella tularensis
Target -1-deoxy-D-xylulose 5-phosphate reductoisomerase (Francisella Tularensis)
Homology Model needed - Christina - DONE
Template: 3ANM
Sequence Identities = 48% , Positives = 66%
Template: Clash score = 17.46, Molprobity score = 2.35
Model: Clash score = 8.26, Molprobity score = 2.42
Trypanosoma brucei
Target- Protein Phosphatase 2B
Homology Model needed - Christina (Larry -- Finished first so the one in the folder is Larry's) - DONE
Template:1auia
Sequence Identities =44% , Positives = 62%
Template: Clash score = 14.64, Molprobity score = 2.42
Model: Clash score = 4.07, Molprobity score = 2.29
Plasmodium falciparans
Target - 1-deoxy-D-xylulose-5-phosphate reductoisomerase (P. falciparum)-
PDB = 3AU8, 3AU9, 3AUA - SADHANA - DONE
Clash score, Molprobity score = 10.48, 1.99
Clash score, Molprobity score = 8.29, 1.98
Clash score, Molprobity score = 11.65, 2.11
Staphylococcus agalactiae - Neonatal Septicemia
Target - S. agalactiae serine-threonine phosphatase STP1
PDB structure available = 2PK0 - Sadhana - DONE
2PK0 Clash score, Molprobity score = 7.53, 1.89
Listeria monocytogenes
Target - Protein Tyrosine Phosphatase (Listeria monocytogenes)
Homology Model needed (Larry) - DONE
Template: 1ywfa,
Sequence Identities = 27% , Positives = 46%
Template: Clash score, Molprobity score = 5.1, 2.03
Model: Clash score, Molprobity score = 0.77, 2.03
Candida albicans
Target - Methionine Synthase (PDB exist) No need.
Template:
Sequence Identities = ? , Positives = ?
Homology Model needed OR PDB structure available?
Template: Clash score, Molprobity score = ???, ???
Model: Clash score, Molprobity score = ???, ???
2011 Targets
Target-Histidine Phosphatase (Francisella Tularensis)Target-MPTPB(Mycobacterium Tuberculosis) H37Rv
Target - Protein-Tyrosine Phosphatase Yersinia pestis YopH (Bubonic Plague)
Target-Mycobacterium Tuberculosis PSTP
Target - Carbonic Anhydrase IX (Homo sapiens)
Target- Carbonic Anhydrase YadF and cynT(E. coli)
Target - PTP1b (Homo sapiens)